BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0001.2542.p (529 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 846 0.0 gi|300313916|ref|YP_003778008.1| two component response regulato... 258 7e-70 gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 253 4e-68 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 250 2e-67 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 243 3e-65 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 846 bits (2185), Expect = 0.0, Method: Compositional matrix adjust. Identities = 458/533 (85%), Positives = 485/533 (90%), Gaps = 11/533 (2%) Query: 1 MTSKALLDALLPLVADLSRDIDDRERYRRLLHSLRALFPCDAAALLRLEGDLLVPLAIDG 60 MTS+ LLDAL+PLVADLSR+IDDRERYRRLL +LR LFPCDAAALLRLEGD+LVPLAIDG Sbjct: 1 MTSRTLLDALVPLVADLSREIDDRERYRRLLQTLRTLFPCDAAALLRLEGDVLVPLAIDG 60 Query: 61 LSSDTLGRRFRIADHPRFGVLLTNAAPTRFPADSPLPDPYDGLVDGLNDAHSGELEVHDC 120 LSSDTLGRRFRI +HPRFG+LL NAAPTRF ADSPLPDPYDGLVDGLND HSGELEVHDC Sbjct: 61 LSSDTLGRRFRITEHPRFGILLGNAAPTRFAADSPLPDPYDGLVDGLNDQHSGELEVHDC 120 Query: 121 MGCALSINGRPWGLMTLDALGPGRFDGVDMASLQAFAALAAATVNVAERINALSQAGEQA 180 MGCAL++NGR WGLMTLDALG GRFD VDM SLQAFAALAAATVNVAERI+ L+QAG+QA Sbjct: 121 MGCALTVNGRAWGLMTLDALGRGRFDRVDMDSLQAFAALAAATVNVAERISDLAQAGQQA 180 Query: 181 RQRAEAYRLGLEESQGKRELIGQSPAQRQLLEEIRMAAPSDMTVLVTGETGTGKELVAHA 240 +QRAEAYRLGLE+SQG+RELIGQSPA RQL++EI MAAPSDMTVLV GETGTGKELVAHA Sbjct: 181 QQRAEAYRLGLEQSQGQRELIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHA 240 Query: 241 LHAASPRAAKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE 300 LHAASPRA KPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE Sbjct: 241 LHAASPRAHKPMISLNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDE 300 Query: 301 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHR 360 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLA+EVKRGHFRADFYHR Sbjct: 301 VGELPLAVQAKLLRVLQSGQLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHR 360 Query: 361 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQHSLLAYPWPGNIREL 420 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQ +LL Y WPGNIREL Sbjct: 361 LSVFPIRVPPLRERGRDVLLLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIREL 420 Query: 421 EHLIGRSALRALAAHPTRPAILTLDAQALELHATDPGPVASAAPVAALAEPS----SDDA 476 EHLIGRSALR+LA H TRP ILTLDA ALEL P S A VAA AEPS S A Sbjct: 421 EHLIGRSALRSLATHRTRPTILTLDAAALEL------PAPSLATVAA-AEPSLPAESTPA 473 Query: 477 PAPDSLRQAVERYERQLVRQSLERNAGNLAAAARELGLDRANLSRLARRLGLR 529 A SLR A+ERYERQLV +L+R+ GNLAA ARELG+DRANL+RLA+RLGLR Sbjct: 474 QASGSLRDALERYERQLVSAALQRHGGNLAATARELGVDRANLNRLAKRLGLR 526 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 258 bits (660), Expect = 7e-70, Method: Compositional matrix adjust. Identities = 157/325 (48%), Positives = 211/325 (64%), Gaps = 19/325 (5%) Query: 197 KRELIGQSPAQRQLLEEIRMAAPSDMTVLVTGETGTGKELVAHALHAASPRAAKPMISLN 256 + +L+G+S A RQ+ ++I AA SD TVLV GETGTGKELVA ALH RAA+P +++N Sbjct: 133 RNQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVN 192 Query: 257 CAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVL 316 CAA+P L+ESELFGHV+GAFSGA + R G+F+ ADGGTLFLDE+G++ LA QAK+LRVL Sbjct: 193 CAAIPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVL 252 Query: 317 QSGQLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHRLSVFPIRVPPLRERGR 376 Q +L VG ++ RVDVR+IAAT+RDL E+ +G FR D ++RL V I VP LRER Sbjct: 253 QERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPG 312 Query: 377 DVLLLAGYFLEQNRARLGLSSLRLSADAQHSLLAYPWPGNIRELEHLIGRSALRALAAHP 436 D+L +A +FL Q G + R+S A LL + WPGN+REL + + R+A+ + Sbjct: 313 DILTIAEHFLRQLG---GDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHG--- 366 Query: 437 TRPAILTLDAQALELHATDPGPVASAAPVAALAEPSSDDAPAPDSLRQAVERYERQLVRQ 496 L ++A+ + L A P ASAA A+ D P L A+ ER ++ + Sbjct: 367 -----LCIEAEDIGLSARPPAGAASAASAPAI------DWDGP--LAVALAEVERVMIER 413 Query: 497 SLERNAGNLAAAARELGLDRANLSR 521 +L+ AGN A AAR LG+ R L R Sbjct: 414 ALQGAAGNRAEAARRLGISRQQLYR 438 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 253 bits (645), Expect = 4e-68, Method: Compositional matrix adjust. Identities = 152/341 (44%), Positives = 202/341 (59%), Gaps = 21/341 (6%) Query: 200 LIGQSPAQRQLLEEIRMAAPSDMTVLVTGETGTGKELVAHALHAASPRAAKPMISLNCAA 259 L+G S A + A +D TVL TGE+G GKE A LH RA + I++NCAA Sbjct: 264 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAA 323 Query: 260 LPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQSG 319 +P+TL+E+ELFG RGA++GA R G+FE+ADGGTLFLDEVG L L Q KLLRVLQ G Sbjct: 324 IPETLIEAELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 383 Query: 320 QLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVL 379 + +RVGS R +VDVR++AATN DLA+ V+ G FR D + RL+VFPI +PPLRER D+ Sbjct: 384 EFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 443 Query: 380 LLAGYFLEQNRARLGLSSLRLSADAQHSLLAYPWPGNIRELEHLIGRSALRALAAHPTR- 438 LL +FL+ R G++ + A +LL Y +PGNIREL++LI R + A HP Sbjct: 444 LLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQNLIERGVILA-QGHPLDL 502 Query: 439 PAILT----LDAQALELHATDPGPVASAAPVAALAEPSSDDAPAP---DSLRQ------- 484 P + L+ + L L + + V E S A D LRQ Sbjct: 503 PHMFISGERLNDEVLSLALQGETGMLAGKSVEKSVEKSVAHPTAQGLLDVLRQWRQEAAG 562 Query: 485 -----AVERYERQLVRQSLERNAGNLAAAARELGLDRANLS 520 + ER+L+ +++ER GNL+AAAR LG+ RA L+ Sbjct: 563 EAAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRAQLA 603 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 250 bits (638), Expect = 2e-67, Method: Compositional matrix adjust. Identities = 155/387 (40%), Positives = 216/387 (55%), Gaps = 15/387 (3%) Query: 138 DALGPGRFDGVDMASLQAFAALAAATVNVAERINALSQAGEQARQRAEAYRLGLEESQGK 197 D P R ++ L A L TV + + A Q Q E R + QGK Sbjct: 144 DGQSPSRSVDHEVRLLTMVANLIGQTVRLYRSVAAERQ------QLQEEKRQLSRQLQGK 197 Query: 198 REL---IGQSPAQRQLLEEIRMAAPSDMTVLVTGETGTGKELVAHALHAASPRAAKPMIS 254 +L IG S A +++ ++ +APS T+L+ GE+GTGKE++A A+H SPR P I Sbjct: 198 YKLDNVIGISKAMQEVFAQVHQSAPSRSTMLLRGESGTGKEVIARAIHYLSPRKDGPFIK 257 Query: 255 LNCAALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLR 314 +NCAAL +TL+ESELFGH +GAF+GA +R+G+FE+A GGTLFLDE+GE+ A QAKLLR Sbjct: 258 VNCAALSETLLESELFGHEKGAFTGAQGERKGRFELAHGGTLFLDEIGEISPAFQAKLLR 317 Query: 315 VLQSGQLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHRLSVFPIRVPPLRER 374 VLQ + +RVG R +VDVRL+ ATNRDL + V +G FRAD Y+R++V I +PPLRER Sbjct: 318 VLQEREFERVGGSRSIKVDVRLVTATNRDLEKAVAKGEFRADLYYRINVVSIFIPPLRER 377 Query: 375 GRDVLLLAGYFLEQNRARLGLSSLRLSADAQHSLLAYPWPGNIRELEHLIGRSALRALAA 434 D+ L +FLE+ R + + +S A ++ WPGN+RELE+ + R+A Sbjct: 378 REDIPYLVEHFLEKFRVENQRAMVAMSPQAMKVMMNCYWPGNVRELENCVERTATMMRGD 437 Query: 435 HPTRPAILTLDAQALELHATDPGP-----VASAAPVAALAEPSSDDAPAPDS-LRQAVER 488 T + L +PG V ++A PSS A D L A Sbjct: 438 LITEVHFSCQQNKCLTKVLHEPGQQQPVVVVPLERISAHTAPSSPSGMAKDKPLAAAPPT 497 Query: 489 YERQLVRQSLERNAGNLAAAARELGLD 515 ER+ + ++E+ A AAR L + Sbjct: 498 SERERLIWAMEQCGWVQAKAARALNIS 524 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 243 bits (620), Expect = 3e-65, Method: Compositional matrix adjust. Identities = 146/360 (40%), Positives = 211/360 (58%), Gaps = 30/360 (8%) Query: 199 ELIGQSPAQRQLLEEIRMAAPSDMTVLVTGETGTGKELVAHALHAASPRAAKPMISLNCA 258 E++GQ+PA + + I + S++TVL+TGE+G+GKELVA ALH SPRA++P ++LN A Sbjct: 135 EILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHSPRASQPFVALNTA 194 Query: 259 ALPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQS 318 A+P L+ESELFGH RGAF+GA A RRG+FE A+GGTLFLDE+G++PL +Q +LLRVL Sbjct: 195 AIPKDLLESELFGHERGAFTGAQAMRRGRFEQAEGGTLFLDEIGDMPLDLQTRLLRVLSD 254 Query: 319 GQLQRVGSDREHRVDVRLIAATNRDLAEEVKRGHFRADFYHRLSVFPIRVPPLRERGRDV 378 G RVG + + +VR+IAAT+++L + V+ G FR D YHRL+V +R+P LRER D+ Sbjct: 255 GHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVIRLRLPSLRERSEDI 314 Query: 379 LLLAGYFLEQNRARLGLSSLRLSADAQHSLLAYPWPGNIRELEHLIGRSAL--------- 429 +LA YFL Q+ +LG+ + RLS A L +PGN+R+LE+L + Sbjct: 315 PILARYFLAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLENLCNWITVMAPGQTVEI 374 Query: 430 ----------RALAAHPTRPAILTLDAQALELHATDPGP--------VASAAPVAALAEP 471 R A P + A AL T+P P A+ A L E Sbjct: 375 KDLPQDLVEERVHAPQPAQTVAAPASAAALPTAYTEPAPGVASASADGAAGASWITLLET 434 Query: 472 SSDDAPA---PDSLRQAVERYERQLVRQSLERNAGNLAAAARELGLDRANLSRLARRLGL 528 + A P+ + ++E L++ +L+ G AA LG+ R ++R + LG+ Sbjct: 435 EAAQMLASEQPEVMDILGRQFEAALIKVALKHTHGRKNDAAVRLGIGRNTITRKIQELGI 494 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.320 0.136 0.390 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,473,040 Number of extensions: 60364 Number of successful extensions: 329 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 311 Number of HSP's successfully gapped: 12 Length of query: 529 Length of database: 1,619,870 Length adjustment: 90 Effective length of query: 439 Effective length of database: 1,193,720 Effective search space: 524043080 Effective search space used: 524043080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 133 (55.8 bits)